I just ran my ipod cable to the armrest of my new stereo on Wednesday.
With my previous stereo I disassembled the whole armrest and it was a total pain - but this time I found an easy way that took me 10 mins.
You can do it by simply pulling the gear gaiter off and taking out the ashtray with 2 x torx screws. Feed the cable from the stereo down to here and then push it through into the drivers footwell.
If you open the armrest and remove the rubber bottom, you should be able to pull open a compartment. Remove 1 x torx screw from above the bit you've just opened and you should be able to loosen off the armrest a bit. Now you can feed the cable directly from your drivers footwell straight into the gap you've made between the armrest / bottle opened compartment - and grab it with your hand and pull it into the armrest.
Tuck the cable up into the center bit, then pull the iPod end and it should pull it all tight so that the cable is no longer visible. With a bit of poking you should be able to get all the cable inside the center bit so that its under the bottle opener bit.